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- PDB-8bsw: IPNS H270Q variant in complex with Fe and ACV under anaerobic con... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bsw | ||||||
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Title | IPNS H270Q variant in complex with Fe and ACV under anaerobic conditions | ||||||
![]() | Isopenicillin N synthase | ||||||
![]() | OXIDOREDUCTASE / Isopenicillin N synthase / antiobiotic biosynthesis / penicillin / beta lactam / oxygenase / anaerobic | ||||||
Function / homology | ![]() isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rabe, P. / Schofield, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: IPNS H270Q variant in complex with Fe and ACV under anaerobic conditions Authors: Rabe, P. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.8 KB | Display | ![]() |
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PDB format | ![]() | 159.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 879.2 KB | Display | ![]() |
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Full document | ![]() | 879.5 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zaeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37553.820 Da / Num. of mol.: 1 / Mutation: H270Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACV / | #4: Chemical | ChemComp-FE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 % / Description: needle morphology, 4 um x 4 um x 200 um |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 19, 2022 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9227 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.58→41.78 Å / Num. obs: 43137 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.066 / Rrim(I) all: 0.244 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZAE Resolution: 1.58→41.73 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.67 Å2 / Biso mean: 26.334 Å2 / Biso min: 14.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→41.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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